NEW: We changed the default behavior of save_tmp (now False). Pass --save_tmp for retrocompatibility
NEW: We changed the default beavior of save_panda_results. Now all PANDA outputs have column headers by default. Pass old_compatible for the previous behavior
Input data:
Expression: tcga_coad_cms1.nodot.txt
Motif data: /home/ubuntu/tcga-coad-subtype/priors/MotifPriorGencode_p5.txt
PPI data: /home/ubuntu/tcga-coad-subtype/priors/ppi_Gencode_p5.txt
Start Panda run ...
Loading motif data ...
  Elapsed time: 2.97 sec.
Loading expression data ...
  Elapsed time: 0.23 sec.
Loading PPI data ...
Number of PPIs: 138479
  Elapsed time: 0.05 sec.
Calculating coexpression network ...
  Elapsed time: 4.19 sec.
Creating motif network ...
  Elapsed time: 3.57 sec.
Creating PPI network ...
  Elapsed time: 0.11 sec.
intersection /home/ubuntu/tcga-coad-subtype/priors/MotifPriorGencode_p5.txt tcga_coad_cms1.nodot.txt /home/ubuntu/tcga-coad-subtype/priors/ppi_Gencode_p5.txt False False False
Normalizing networks ...
  Elapsed time: 25.22 sec.
Running PANDA algorithm ...
Computing panda on CPU
step: 0, hamming: 3.7554531004950227
step: 1, hamming: 0.7714061840873245
step: 2, hamming: 0.6233205987286476
step: 3, hamming: 0.5608977847818664
step: 4, hamming: 0.5131679514729571
step: 5, hamming: 0.4682568011749086
step: 6, hamming: 0.4239020455974748
step: 7, hamming: 0.38025316018861816
step: 8, hamming: 0.33805416725154
step: 9, hamming: 0.29806022241583663
step: 10, hamming: 0.2608472516471065
step: 11, hamming: 0.2267733589592256
step: 12, hamming: 0.19599860949128048
step: 13, hamming: 0.1685249883399891
step: 14, hamming: 0.1442394640009216
step: 15, hamming: 0.12295204273029446
step: 16, hamming: 0.10442674098203582
step: 17, hamming: 0.08840518206197198
step: 18, hamming: 0.07462369177988236
step: 19, hamming: 0.06282502640419439
step: 20, hamming: 0.05276591588964592
step: 21, hamming: 0.044221513973253475
step: 22, hamming: 0.03698761721689259
step: 23, hamming: 0.030881303552494712
step: 24, hamming: 0.0257405298720037
step: 25, hamming: 0.02142305330588777
step: 26, hamming: 0.01780496132532951
step: 27, hamming: 0.014779011163607518
step: 28, hamming: 0.012252905258663094
step: 29, hamming: 0.010147594733912696
step: 30, hamming: 0.00839566708258172
step: 31, hamming: 0.0069398511058069955
step: 32, hamming: 0.005731655758810202
step: 33, hamming: 0.0047301485613811785
step: 34, hamming: 0.003900872287998611
step: 35, hamming: 0.003214892326284277
step: 36, hamming: 0.0026479663709063268
step: 37, hamming: 0.002179825118083652
step: 38, hamming: 0.0017935527988847946
step: 39, hamming: 0.0014750564363724596
step: 40, hamming: 0.0012126130962286084
step: 41, hamming: 0.0009964852176471794
Running panda took: 703.26 seconds!
Saving PANDA network to panda_tcga_coad_cms1.txt ...
WARNING: panda is now saved with the column names. 
Use old_compatible=True to save the panda results as previous versions without header
  Elapsed time: 45.35 sec.
